Mercurial > repos > marpiech > norwich_tools_docking2
diff tools/rdock/data/masses.rtf @ 3:279ba0732f87 draft default tip
planemo upload
| author | marpiech |
|---|---|
| date | Mon, 29 Aug 2016 09:07:58 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rdock/data/masses.rtf Mon Aug 29 09:07:58 2016 -0400 @@ -0,0 +1,180 @@ +* ... +* ... +* Copyright (c) 1986, 1987, 1988, 1989, 1990, 1991, 1992 +* Molecular Simulations Incorporated +* Confidential and Proprietary: All Rights Reserved +* ... +* .... +* TEMPLATE FOR CREATING CHARMm RTF file +* .... +* (%_m) replaced by first 4 characters of molecule name +* in QUANTA (if used) +* .. +* Build RTF for %m +* ... +* sorted alphabetically; metals follow organics +* Atom type numbers 201-229 are reserved for special QUANTA display atom types. +* Last current active number is 234. +* + 22 0 +MASS 7 B 10.81 B ! Boron +MASS 14 C 12.01100 C ! Carbonyl or Guanidinium carbon (RBT::SP2) +MASS 190 C3 12.01100 C ! Carbonyl carbon in 3-membered aliphatic ring (RBT::SP2) +MASS 192 C4 12.01100 C ! Carbonyl carbons in 4-membered aliphatic ring (RBT::SP2) +MASS 21 C5R 12.01100 C ! Aromatic carbon in a five membered ring (RBT::SP2) +MASS 23 C5RE 13.01900 C ! Extended aromatic carbon in five membered ring (RBT::SP2) +MASS 28 C5RP 12.01100 C ! for Aryl-Aryl bond between C5R rings (RBT::SP2) +MASS 189 C5RQ 12.01100 C ! for second Ar-Ar bond between C5RP rings (ortho) (RBT::SP2) +MASS 22 C6R 12.01100 C ! Aromatic carbon in a six membered ring (RBT::SP2) +MASS 24 C6RE 13.01900 C ! Extended aromatic carbon in six membered ring (RBT::SP2) +MASS 29 C6RP 12.01100 C ! for Aryl-Aryl bond between C6R rings (RBT::SP2) +MASS 194 C6RQ 12.01100 C ! Carbon of C6RP type ortho to C6RP pair (RBT::SP2) +MASS 230 CF1 12.01100 C ! Carbon with one Fluorine (RBT::SP3) +MASS 231 CF2 12.01100 C ! Carbon with two Fluorines (RBT::SP3) +MASS 232 CF3 12.01100 C ! Carbons with three Fluorines (RBT::SP3) +MASS 11 CH1E 13.01900 C ! Extended atom carbon with one hydrogen (RBT::SP3) +MASS 12 CH2E 14.02700 C ! Extended atom carbon with two hydrogens (RBT::SP3) +MASS 13 CH3E 15.03500 C ! Extended atom carbon with three hydrogens (RBT::SP3) +MASS 15 CM 12.01100 C ! Carbonmonoxide, or other triply bonded, carbon (RBT::SP) +MASS 199 CP3 12.01100 C ! Carbon on nitrogen in proline ring (RBT::SP3) +MASS 197 CPH1 12.01100 C ! CG and CD2 carbons in histidine ring (RBT::SP2) +MASS 198 CPH2 12.01100 C ! CE1 carbon in histidine ring (RBT::SP2) +MASS 195 CQ66 12.01100 C ! Third adjacent pair of CR66 types in fused rings (RBT::SP2) +MASS 25 CR55 12.01100 C ! Aromatic carbon-merged five membered rings (RBT::SP2) +MASS 26 CR56 12.01100 C ! Aromatic carbon-merged five/six membered rings (RBT::SP2) +MASS 27 CR66 12.01100 C ! Aromatic carbon-merged six membered rings (RBT::SP2) +MASS 196 CS66 12.01100 C ! Second adjacent pair of CR66 types in fused rings (RBT::SP2) +MASS 10 CT 12.01100 C ! Aliphatic carbon (tetrahedral) (RBT::SP3) +MASS 191 CT3 12.01100 C ! in 3-membered aliphatic ring, usually tetrahedral (RBT::SP3) +MASS 193 CT4 12.01100 C ! in 4-membered aliphatic ring, usually tetrahedral (RBT::SP3) +MASS 16 CUA1 12.01100 C ! Carbon in double bond, first pair (RBT::SP2) +MASS 17 CUA2 12.01100 C ! Carbon in double bond, second conjugated pair (RBT::SP2) +MASS 20 CUA3 12.01100 C ! Carbon in double bond, third conjugated pair (RBT::SP2) +MASS 18 CUY1 12.01100 C ! Carbon in triple bond, first pair (RBT::SP) +MASS 19 CUY2 12.01100 C ! Carbon in triple bond, second conjugated pair (RBT::SP) +MASS 1 H 1.00800 H ! Hydrogen bonding hydrogen (neutral group) (RBT::SP3) +MASS 3 HA 1.00800 H ! Aliphatic or aromatic hydrogen (RBT::SP3) +MASS 2 HC 1.00800 H ! Hydrogen bonding hydrogen (charged group) (RBT::SP3) +MASS 9 HMU 1.00800 H ! Mu-bonded hydrogen for metals and boron-hydride (RBT::SP3) +MASS 8 HO 1.00800 H ! Hydrogen on an alcohol oxygen (RBT::SP3) +MASS 4 HT 1.00800 H ! TIPS3P water model hydrogen (RBT::SP3) +MASS 31 N 14.00670 N ! Nitrogen; planar-valence of 3, i.e. nitrile, etc. (RBT::TRI) +MASS 234 N3 14.00670 N ! Nitrogen in a three membered ring (RBT::SP3) +MASS 34 N5R 14.00670 N ! Nitrogen in a five membered aromatic ring (RBT::TRI) +MASS 30 N5RP 14.00670 N ! for Ar-Ar bond between five membered rings (RBT::TRI) +MASS 35 N6R 14.00670 N ! Nitrogen in a six membered aromatic ring (RBT::SP2) +MASS 39 N6RP 14.00670 N ! for Aryl-Aryl bond between six membered rings (RBT::SP2) +MASS 37 NC 14.00670 N ! Charged guanidinium-type nitrogen (RBT::TRI) +MASS 186 NC2 14.00670 N ! for neutral guanidinium group - Arg sidechain (RBT::SP2) +MASS 38 NO2 14.00670 N ! Nitrogen in nitro, or related, group (RBT::TRI) +MASS 32 NP 14.00670 N ! Nitrogen in peptide, amide, or related, group (RBT::TRI) +MASS 183 NR1 14.00670 N ! Protonated nitrogen in neutral histidine ring (RBT::TRI) +MASS 184 NR2 14.00670 N ! Unprotonated nitrogen in neutral histidine ring (RBT::SP2) +MASS 185 NR3 14.00670 N ! Nitrogens in charged histidine ring (RBT::SP2) +MASS 182 NR55 14.00670 N ! N at fused bond between two 5-membered aromatics (RBT::SP2) +MASS 180 NR56 14.00670 N ! N at fused bond between 5 and 6-membered aryls (RBT::SP2) +MASS 181 NR66 14.00670 N ! N at fused bond between two 6-membered aromatics (RBT::SP2) +MASS 36 NT 14.00670 N ! Nitrogen (tetrahedral), i.e. Amine, etc. (RBT::SP3) +MASS 33 NX 14.00670 N ! Proline nitrogen, or similar (RBT::TRI) +MASS 40 O 15.99940 O ! Carbonyl oxygen for amides, or related structures (RBT::SP2) +MASS 56 O2M 15.99940 O ! Oxygen in Si-O-Al or Al-O-Al bond (RBT::SP3) +MASS 52 O5R 15.99940 O ! Oxygen in 5 membered aromatic ring-radicals, etc. (RBT::SP3) +MASS 53 O6R 15.99940 O ! Oxygen in 6 membered aromatic ring-radicals, etc. (RBT::SP3) +MASS 41 OA 15.99940 O ! Carbonyl oxygen for aldehydes, or related (RBT::SP2) +MASS 51 OAC 15.99940 O ! Carbonyl oxygen for acids, or related (RBT::SP2) +MASS 43 OC 15.99940 O ! Charged oxygen (RBT::SP3) +MASS 50 OE 15.99940 O ! Ether oxygen / Acetal oxygen (RBT::SP3) +MASS 47 OH2 15.99940 O ! ST2 water model oxygen (RBT::SP3) +MASS 42 OK 15.99940 O ! Carbonyl oxygen for ketones, or related (RBT::SP2) +MASS 48 OM 15.99940 O ! Carbonmonoxide, or other triply bonded, oxygen +MASS 49 OS 15.99940 O ! Ester oxygen (RBT::TRI) +MASS 57 OSH 0.00000 O ! Massless O for zeolites, or related cage cmpds. +MASS 55 OSI 15.99940 O ! Oxygen in Si-O-Si bond (RBT::SP3) +MASS 45 OT 15.99940 O ! Hydroxyl oxygen (tetrahedral) or Ionizable acid (RBT::SP3) +MASS 46 OW 15.99940 O ! TIP3P water model oxygen (RBT::SP3) +MASS 64 P6R 30.9738 P ! Phosphorous in aromatic 6-membered ring (RBT::SP3) +MASS 61 PO3 30.9738 P ! Phosphorous bonded to three oxygens (RBT::SP2) +MASS 62 PO4 30.9738 P ! Phosphorous bonded to four oxygens (RBT::SP2) +MASS 60 PT 30.9738 P ! Phosphorous, general; usually tetrahedral (RBT::SP3) +MASS 63 PUA1 30.9738 P ! Phosphorous double bond +MASS 233 PUY1 30.9738 P ! Triple bonded phosphorus +MASS 72 S5R 32.0600 S ! Sulphur in a five membered aromatic ring (RBT::SP3) +MASS 73 S6R 32.0600 S ! Sulphur in a six membered aromatic ring (RBT::SP3) +MASS 74 SE 32.060 S ! Thioether sulphur (RBT::SP3) +MASS 71 SH1E 33.06800 S ! Extended atom sulphur with one hydrogen (RBT::SP3) +MASS 75 SK 32.060 S ! Thioketone sulphur (RBT::SP2) +MASS 76 SO1 32.0600 S ! Sulphur bonded to one oxygen (RBT::SP3) +MASS 77 SO2 32.0600 S ! Sulphur bonded to two oxygens (RBT::SP3) +MASS 78 SO3 32.0600 S ! Sulphur bonded to three oxygens (RBT::SP2) +MASS 79 SO4 32.0600 S ! Sulphur bonded to four oxygens (RBT::SP2) +MASS 70 ST 32.06000 S ! Sulphur, general; usually tetrahedral (RBT::SP3) +MASS 94 XBR 79.904 Br ! Bromine +MASS 93 XCL 35.45300 Cl ! Chlorine +MASS 92 XF 18.99840 F ! Fluorine +MASS 95 XI 126.9045 I ! Iodine +MASS 91 MAL 26.9815 Al ! ALuminum +MASS 6 MBE 9.01218 Be ! Beryllium +MASS 84 MCA 40.080 Ca ! Calcium +MASS 83 MK 39.098 K ! Potassium +MASS 80 MLI 6.941 Li ! Lithium +MASS 82 MMG 24.305 Mg ! Magnesium +MASS 81 MNA 22.9898 Na ! Sodium +MASS 90 MSI 28.0855 Si ! Silicon +MASS 177 MSIU 28.08550 Si ! Silicon when as double bond +MASS 86 MFE 55.85 Fe ! Iron +MASS 87 MZN 65.3800 Zn ! Zinc (Added DM 30/7/2001) + +* 4 Jan 1999 (DM) Added old types from +* /darius/dsk1/progs/insightII/insight97/data/xplor/toppar/topallhdg.pro +* just to keep rbscore happy. The numeric force field types are ficticious +* and will not be recognised by Charmm +MASS 301 CX 12.011 C ! (RBT::SP2) +MASS 302 CW 12.011 C ! (RBT::SP2) +MASS 303 CN 12.011 C ! (RBT::SP2) +MASS 304 CA 12.011 C ! (RBT::SP2) +MASS 305 CB 12.011 C ! (RBT::SP2) +MASS 306 CC 12.011 C ! (RBT::SP2) +MASS 307 CV 12.011 C ! (RBT::SP2) +MASS 308 CR 12.011 C ! (RBT::SP2) +MASS 309 CP 12.011 C ! Proline carbon CG,CD (RBT::SP3) +MASS 310 NA 14.007 N ! (RBT::TRI) +MASS 311 NB 14.007 N ! (RBT::TRI) +MASS 312 NH1 14.007 N ! (RBT::TRI) +MASS 313 NH2 14.007 N ! (RBT::TRI) +MASS 314 NH3 14.007 N ! (RBT::SP3) +MASS 315 OH 15.999 O ! (RBT::SP3) +MASS 316 S 32.060 S ! (RBT::SP3) + +* 4 Jan 1999 (DM) Added old types from +* /darius/dsk1/progs/insightII/insight97/data/xplor/toppar/topallhdg.dna +* just to keep rbscore happy. The numeric force field types are ficticious +* and will not be recognised by Charmm +MASS 400 H2 1.00800 H ! (RBT::SP3) +MASS 401 CH 12.01100 C ! (RBT::SP3) +MASS 402 C2 12.01100 C ! (RBT::SP3) +MASS 403 CE 12.01100 C ! (RBT::SP2) +MASS 404 CF 12.01100 C ! (RBT::SP2) +MASS 405 CS 12.01100 C ! (RBT::SP2) +MASS 406 N2 14.00670 N ! (RBT::TRI) Corrected DM 23/8/1999 +MASS 407 NS 14.00670 N ! (RBT::TRI) +MASS 408 NH2E 16.02270 N ! (RBT::SP3) +MASS 409 O2 15.99940 O ! (RBT::SP3) +MASS 411 SD 22.98980 Na ! +MASS 412 P 30.97400 P ! (RBT::SP3) +MASS 413 BR 79.90400 Br ! +MASS 414 MG 24.30500 Mg ! + +* 8 Jun 1999 (DM) Added types to keep wtTARrbt158.psf happy +MASS 450 HE 1.00800 H ! (RBT::SP3) + +* 18 Jan 2001 (DM) Dummy atom type +MASS 666 DUM 0.00000 DU ! Dummy atom + +* Charmm 27 additions +MASS 5 H 1.00800 H ! Nonpolar H prom charmm27 all-atom FF (RBT::SP3) +MASS 54 HG 1.00800 H ! Nonpolar H prom charmm27 all-atom FF (RBT::SP3) +MASS 58 NE 14.00670 N ! charmm27 N + +RESI XXXX 0.0 + +END